Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium Lactobacillus sakei▿ †

Lactobacillus sakei is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing L. sakei subspecies (sakei and carnosus). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in L. sakei. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products

The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K

The sequence reported in this paper has been deposited in the EMBL database as Accession No. CR936503. The annotated genome sequence and the relevant AGMIAL database (Genome navigator, BLAST server and Metabolic comparison) are available at http://migale.jouy.inra.fr/sakei/.International audienceLactobacillus sakei is a psychrotrophic lactic acid bacterium found naturally on fresh meat and fish. This microorganism is widely used in the manufacture of fermented meats and has biotechnological potential in biopreservation and food safety. We have explored the 1,884,661-base-pair (bp) circular chromosome of strain 23K encoding 1,883 predicted genes. Genome sequencing revealed a specialized metabolic repertoire, including purine nucleoside scavenging that may contribute to an ability to successfully compete on raw meat products. Many genes appear responsible for robustness during the rigors of food processing – particularly resilience against changing redox and oxygen levels. Genes potentially responsible for biofilm formation and cellular aggregation that may assist the organism to colonize meat surfaces were also identified. This genome project is an initial step for investigating new biotechnological approaches to meat and fish processing and for exploring fundamental aspects of bacterial adaptation to these specific environments

Meiotic recombination analyses in pigs carrying different balanced structural chromosomal rearrangements

Correct pairing, synapsis and recombination between homologous chromosomes are essential for normal meiosis. All these events are strongly regulated, and our knowledge of the mechanisms involved in this regulation is increasing rapidly. Chromosomal rearrangements are known to disturb these processes. In the present paper, synapsis and recombination (number and distribution of MLH1 foci) were studied in three boars (Sus scrofa domestica) carrying different chromosomal rearrangements. One (T34he) was heterozygote for the t(3;4)(p1.3;q1.5) reciprocal translocation, one (T34ho) was homozygote for that translocation, while the third (T34Inv) was heterozygote for both the translocation and a pericentric inversion inv(4)(p1.4;q2.3). All three boars were normal for synapsis and sperm production. This particular situation allowed us to rigorously study the impact of rearrangements on recombination. Overall, the rearrangements induced only minor modifications of the number of MLH1 foci (per spermatocyte or per chromosome) and of the length of synaptonemal complexes for chromosomes 3 and 4. The distribution of MLH1 foci in T34he was comparable to that of the controls. Conversely, the distributions of MLH1 foci on chromosome 4 were strongly modified in boar T34Inv (lack of crossover in the heterosynaptic region of the quadrivalent, and crossover displaced to the chromosome extremities), and also in boar T34ho (two recombination peaks on the q-arms compared with one of higher magnitude in the controls). Analyses of boars T34he and T34Inv showed that the interference was propagated through the breakpoints. A different result was obtained for boar T34ho, in which the breakpoints (transition between SSC3 and SSC4 chromatin on the bivalents

Meiotic recombinaison analyses of individual chromosomes in male domestic pigs (sus scrofa domestica)

For the first time in the domestic pig, meiotic recombination along the 18 porcine autosomes was directly studied by immunolocalization of MLH1 protein. In total, 7,848 synaptonemal complexes from 436 spermatocytes were analyzed, and 13,969 recombination sites were mapped. Individual chromosomes for 113 of the 436 cells (representing 2,034 synaptonemal complexes) were identified by immunostaining and fluorescence in situ hybridization (FISH). The average total length of autosomal synaptonemal complexes per cell was 190.3 µm, with 32.0 recombination sites (crossovers), on average, per cell. The number of crossovers and the lengths of the autosomal synaptonemal complexes showed significant intra- (i.e. between cells) and inter-individual variations. The distributions of recombination sites within each chromosomal category were similar: crossovers in metacentric and submetacentric chromosomes were concentrated in the telomeric regions of the p- and q-arms, whereas two hotspots were located near the centromere and in the telomeric region of acrocentrics. Lack of MLH1 foci was mainly observed in the smaller chromosomes, particularly chromosome 18 (SSC18) and the sex chromosomes. All autosomes displayed positive interference, with a large variability between the chromosomes

Number of spermatocytes analyzed, mean MLH1 foci numbers and relative SC length per spermatocyte.

<p>Number of spermatocytes analyzed, mean MLH1 foci numbers and relative SC length per spermatocyte.</p

Relationship between the two distances from breakpoint to the nearest CO on the left [d(L)] and right [d(R)] sides of chromosomes that have at least one CO on each side.

<p>The results of the correlation analyses are indicated for each boar. The distances are expressed as percentage of the SC length.</p

Graph of interference strength values (see Methods) for the indicated interval pairs in boars T34ho and controls.

<p>The arrows represent the putative location of the breakpoints on the der(3) and der(4) chromosomes.</p

GTG banding and synapsis at meiosis-I for each chromosomal rearrangement.

<p>(a) GTG banding of the chromosomes involved in the rearrangements. The dotted lines in red represent the breakpoints locations. (b) Identification of chromosome arms on spermatocytes after FISH of BAC clones (more details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154635#pone.0154635.s001" target="_blank">S1 Fig</a>) and immunolocalization of SCP1-SCP3 (red), MLH1 (green) and kinetochores (blue). (c) Schematic representation of the synapsis between chromosomes. The dotted lines in red represent the normal synapsis, the dotted line in black the heterosynapsis, the white rectangles represent the SSC3 chromatin and the grey rectangles the SSC4 chromatin, the black ovals represent the centromeres and the black lines on the T34Inv represent the breakpoints.</p

Comparison of the MLH1 distributions between rearranged chromosomes and controls.

<p>The y-axis indicates the frequency of the MLH1 signals along the SCs on the controls (in blue) and on the rearranged chromosomes (in red). The x-axis represents the length of the SCs in percent from the q (left) arm to the p (right) arm. The vertical lines in bold represent the centromeres and the dotted line represents the estimated position of the breakpoints on the translocated chromosomes.</p